RetrogeneDB ID: retro_ocun_1829

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019135:128609..129170(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023376
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSOCUG00000000074
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_ocun_1829
ATGGGTAAAGGAGACCCCAACAAGCCAAGGGGCAAAATGTCCTCCTATGCCTTCTTCGTGCAGACGTGCCGGGAAGAGCA
CAAGAAGAAACACCCTGACTCTTCGGTCAATTTCGCAGAATTCTCTAAGAAATGCTCGGAGAGATGGAAGACCATGTCTG
CAAAGGAAAAGTCCAAGTTTGAAGATATGGCAAAAAGTGAAAAAGCTCGTTATGACAGGGAGATGAAAAATTACGTTCCT
CCCAAGGGTGATAAGAAGGGAAAGAAAAAGGATCCCAATGCTCCTAAAAGACCACCATCTGCCTTCTTTCTCTTTTGCTC
TGAACATCGCCCAAAGATCAAAAGTGAACACCCTGGCCTGTCCATTGGGGACACTGCAAAAAAATTGGGTGAGATGCGGT
CTGAACACTCAGCCAAAGATAAACAACCATATGAACAGAAAGCAGCTAAGCTAAAGGAGAAATATGAAAAGGATATTGCT
GCATACCGTGCCAAGGGCAAAAGTGAAGCGGGAAAGAAGGGCCCTGGTAGGCCCACAGGCTCAAACAAGAAGAATGAACC
T

Alignment

ORF - retro_ocun_1829 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 89.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKAR
          MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKS.KAR
Retrocopy MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSEKAR

Parental  YDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKD
          YDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEM.SE.SAKD
Retrocopy YDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMRSEHSAKD

Parental  KQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGSKKKNEP
          KQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGS.KKNEP
Retrocopy KQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGSNKKNEP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	6.57 RPM
SRP017611_kidney	0.00 RPM	7.50 RPM
SRP017611_liver	0.00 RPM	1.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1829 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555, retro_cjac_832,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Loxodonta africana	ENSLAFG00000010417	3 retrocopies	retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Myotis lucifugus	ENSMLUG00000026303	4 retrocopies	retro_mluc_1113, retro_mluc_1381, retro_mluc_1726, retro_mluc_2011,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Mustela putorius furo	ENSMPUG00000001919	9 retrocopies	retro_mputfur_1134, retro_mputfur_1167, retro_mputfur_1379, retro_mputfur_1475, retro_mputfur_1631, retro_mputfur_1633, retro_mputfur_1644, retro_mputfur_940, retro_mputfur_989,
Mus musculus	ENSMUSG00000054717	23 retrocopies	retro_mmus_1477, retro_mmus_1745, retro_mmus_1974, retro_mmus_1975, retro_mmus_2269, retro_mmus_2527, retro_mmus_2528, retro_mmus_2529, retro_mmus_2530, retro_mmus_2531, retro_mmus_2843, retro_mmus_2884, retro_mmus_3248, retro_mmus_3426, retro_mmus_461, retro_mmus_626, retro_mmus_642, retro_mmus_796, retro_mmus_861, retro_mmus_901, retro_mmus_902, retro_mmus_904, retro_mmus_905,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829 ,
Oryctolagus cuniculus	ENSOCUG00000005986	7 retrocopies	retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Oryctolagus cuniculus	ENSOCUG00000021335	16 retrocopies	retro_ocun_1039, retro_ocun_1112, retro_ocun_1368, retro_ocun_1407, retro_ocun_1554, retro_ocun_1658, retro_ocun_1739, retro_ocun_1882, retro_ocun_1937, retro_ocun_285, retro_ocun_36, retro_ocun_471, retro_ocun_616, retro_ocun_633, retro_ocun_737, retro_ocun_825,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Pteropus vampyrus	ENSPVAG00000014656	1 retrocopy	retro_pvam_872,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Ictidomys tridecemlineatus	ENSSTOG00000023980	2 retrocopies	retro_itri_1720, retro_itri_880,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,